MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.


Model : iML1515 [2].
Target metabolite : hdca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3831 b2744 b3614 b0910 b3752 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b2361 b2291 b0411 b2342 b3845 b4138 b4123 b0621 b0452 b2197 b3918 b1912 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.652257 (mmol/gDw/h)
  Minimum Production Rate : 0.344486 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.366408
  EX_o2_e : 270.373149
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.969415
  EX_pi_e : 0.629171
  EX_so4_e : 0.164251
  EX_k_e : 0.127316
  EX_mg2_e : 0.005658
  EX_ca2_e : 0.003395
  EX_cl_e : 0.003395
  EX_cu2_e : 0.000462
  EX_mn2_e : 0.000451
  EX_zn2_e : 0.000222
  EX_ni2_e : 0.000211
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989524
  EX_h2o_e : 543.357170
  EX_co2_e : 23.145198
  EX_succ_e : 0.680169
  EX_ura_e : 0.462547
  Auxiliary production reaction : 0.344486
  DM_5drib_c : 0.000147
  DM_4crsol_c : 0.000145

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.


Last updated: 21-Sep-2023
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